tumour dna test paves the way to customized cancer treatment

Blood tests derived from the DNA of cancer patients’ tumors will offer doctors a new way to determine whether the patients’ treatment has eliminated the disease, a study said.

Scientists at the Johns Hopkins Kimmel Cancer Center and Life Technologies, a Carlsbad, Calif.-based biotechnology company, scanned the genomes of six cancer patients, looking for large chunks of rearranged DNA. These alterations occur in cancer cells but not in healthy tissue. By using these gene sequences to create biomarkers, or “red flags”, the researchers were able to see whether the patients’ blood, tested after treatment, contained any traces of DNA from the tumor.

These blood tests may give oncologists a clearer picture of how a patient is responding to treatment, according to a report published online this week in the journal Science Translational Medicine. The blood tests may alert doctors to a recurrence of cancer earlier than commonly used imaging tools, such as CT scans, would detect it.

“This is going to have huge implications in cancers where there are no biomarkers,” said Luis Diaz, a cancer specialist at Johns Hopkins Hospital in Baltimore, in a telephone interview.

“When we give a therapy like surgery or radiation, we have no good way of differentiating who was cured. It’s becoming clearer with novel biomarkers like this.”

The researchers are refining the technique to make a ‘commercially viable’ genome-based blood test, according to a statement from Johns Hopkins.

The researchers took samples of solid-tumor tissue and healthy cells from four patients with colorectal cancer and two with breast cancer. They used a next-generation gene-sequencing technology to sequence multiple fragments of DNA in parallel.

Scientists think tumors have DNA rearrangements not present in normal blood and tissue, according to the report. Diaz describes this as ‘a sort of erosion of the genome’ as the cancer grows. In each of the tumor samples, the researchers found at least four confirmed regions where there was incorrect ordering or orientation of DNA sequences.

These unique sequences were used to create telltale biomarkers. When the researchers took blood samples from the patients, they were able to search for these “red flags” to hunt down residual tumor DNA.

The main barrier to using this in cancer patients is the high cost of sequencing the genome, according to the report. A genome scan currently costs about $5,000 per patient, whereas a CT scan is priced about $1,500, the paper said.

The cost of sequencing continues to come down, however. In November, Complete Genomics, a closely held Mountain View, Calif.-based company, produced complete sequences of three people’s DNA at an average cost of $4,500.

Illumina Inc., the San Diego-based maker of DNA analysis equipment, has a new system called HiSeq2000, which can decipher a person’s entire genetic code for less than $10,000. Two years ago, the company said, it took four weeks and cost $100,000 to sequence a human genome.

“If you envision that sequencing is going to come down in price to $1,000 or less, this test becomes a huge cost saver,” said Diaz.

Another way the tests may bring down the cost of medical care is by sparing post-surgical patients the need for costly chemotherapy treatments when the blood exam shows the cancer has been eliminated by surgery alone, he said.

A potential application of this approach may be to use blood tests for cancer screening, Diaz said. One problem is that unlike testing for mutations that are common to certain cancers, scientists don’t know which DNA rearrangements to look for because they vary from one individual to another.

“It’s like looking for a criminal without knowing his fingerprint,” Diaz said.

The StarPhoenix (Saskatoon)
Sat Feb 20 2010
Page: C14
Section: World
Source: Bloomberg News